aspirincode / thermalizer

thermalizer

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Automated translation from mesophilic AA sequence to thermally stabilized variant

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Some notes:

• The environment for this tool can be reconstructed with conda. It is saved in environment.yml
• Requires python 3.6

Overview of files:

File	Description
P1_TableGenerator.py	Extracts all protein sequences from the refseq bacterial and archeael genomes.
P2_Table2Fasta	Creates a fasta file with the protein sequences from P1.
P3_16S_TableGenerator.py	Extracts 16sRNA sequences from the genome.
P4_split_data.py	Splits 16sRNA sequences into thermophilic and mesophilic.
P4_16S_blast.py	Aligns 16sRNA sequences.
P5_best_hit.py	For each thermophile find its best hit among mesophiles.
P6_append_protein.py	Appends corresponding proteins to P5.
P7_blastp_njobs.py	Aligns protein sequences from P6
P8_blastp_best_hit.py	For each thermophilic protein find its best hit among mesophilic proteins.
P9_blastp_seq_pair.py	Appends sequences according to protein ids from P8.
P10_s2s_pytorch.py	Defines the modules for data preprocessing and training.
pytorchtools.py	Defines the classes for Encoder, Attention Mechanism, Decoder, EarlyStopping and InferenceDecoder.
Seq2Seq_in_Pytorch.ipynb	The NLP Demo for a small sample.